The invention belongs to the field of physical experiment equipment of petroleum and natural gas exploitation, and particularly relates to a heterogeneous reservoir water injection commingling interlayer disturbance simulation system. The system comprises a constant-flux pump, a plurality of containers, a five-way valve, a core holding unit, an X-ray tube, a detector and a data processing and imaging system. The constant-flux pump is connected with the inlet of each container through pipelines; the inlet of the five-way valve is respectively connected with the outlet of each container through pipelines. A left sealing cover of the core holding unit is provided with an injection port, the right sealing cover of the core holding unit is provided with an output port, the inner sides of the left sealing cover and the right sealing cover are sequentially provided with a core end cap rubber mat, a core end cap and a sealing rubber mat from outside to inside, a plurality of circular holes are formed in the core end cap rubber mat, and the core end cap and the sealing rubber mat are provided with a plurality of layer chambers. A plurality of layers of heterogeneous reservoir slab models are arranged in a sealing rubber sleeve. The outlet of the five-way valve is connected with the injection port, and fluid passes through the output port and enters a measuring cylinder. The heterogeneous reservoir water injection commingling layer disturbance simulation system can reflect layer disturbance degree through the composition and size of liquid amount at the output end, and visualized analysis is achieved.